IsoSpec 2.2.1
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Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Friends | List of all members
IsoSpec::FixedEnvelope Class Reference

Public Member Functions

 FixedEnvelope (const FixedEnvelope &other)
 
 FixedEnvelope (FixedEnvelope &&other)
 
 FixedEnvelope (double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN)
 
FixedEnvelope operator+ (const FixedEnvelope &other) const
 
FixedEnvelope operator* (const FixedEnvelope &other) const
 
size_t confs_no () const
 
int getAllDim () const
 
const double * masses () const
 
const double * probs () const
 
const int * confs () const
 
double * release_masses ()
 
double * release_probs ()
 
int * release_confs ()
 
void release_everything ()
 
double mass (size_t i) const
 
double prob (size_t i) const
 
const int * conf (size_t i) const
 
void sort_by_mass ()
 
void sort_by_prob ()
 
double get_total_prob ()
 
void scale (double factor)
 
void normalize ()
 
void shift_mass (double shift)
 
void resample (size_t ionic_current, double beta_bias=1.0)
 
double empiric_average_mass ()
 
double empiric_variance ()
 
double empiric_stddev ()
 
double WassersteinDistance (FixedEnvelope &other)
 
double OrientedWassersteinDistance (FixedEnvelope &other)
 
double AbyssalWassersteinDistance (FixedEnvelope &other, double abyss_depth, double other_scale=1.0)
 
std::tuple< double, double, double > WassersteinMatch (FixedEnvelope &other, double flow_distance, double other_scale=1.0)
 
FixedEnvelope bin (double bin_width=1.0, double middle=0.0)
 
template<bool tgetConfs>
void threshold_init (Iso &&iso, double threshold, bool absolute)
 
template<bool tgetConfs, typename GenType = IsoLayeredGenerator>
void addConfILG (const GenType &generator)
 
template<bool tgetConfs>
void total_prob_init (Iso &&iso, double target_prob, bool trim)
 
template<bool tgetConfs>
void stochastic_init (Iso &&iso, size_t _no_molecules, double _precision, double _beta_bias)
 

Static Public Member Functions

static FixedEnvelope LinearCombination (const std::vector< const FixedEnvelope * > &spectra, const std::vector< double > &intensities)
 
static FixedEnvelope LinearCombination (const FixedEnvelope *const *spectra, const double *intensities, size_t size)
 
static FixedEnvelope FromThreshold (Iso &&iso, double threshold, bool absolute, bool tgetConfs=false)
 
static FixedEnvelope FromThreshold (const Iso &iso, double _threshold, bool _absolute, bool tgetConfs=false)
 
static FixedEnvelope FromTotalProb (Iso &&iso, double target_total_prob, bool optimize, bool tgetConfs=false)
 
static FixedEnvelope FromTotalProb (const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false)
 
static FixedEnvelope FromStochastic (Iso &&iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false)
 
static FixedEnvelope FromStochastic (const Iso &iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false)
 
static FixedEnvelope Binned (Iso &&iso, double target_total_prob, double bin_width, double bin_middle=0.0)
 
static FixedEnvelope Binned (const Iso &iso, double target_total_prob, double bin_width, double bin_middle=0.0)
 

Protected Member Functions

template<typename T , bool tgetConfs>
ISOSPEC_FORCE_INLINE void store_conf (const T &generator)
 
ISOSPEC_FORCE_INLINE void store_conf (double _mass, double _prob)
 
template<bool tgetConfs>
ISOSPEC_FORCE_INLINE void swap (size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace)
 
template<bool tgetConfs>
void reallocate_memory (size_t new_size)
 
void slow_reallocate_memory (size_t new_size)
 

Protected Attributes

double * _masses
 
double * _probs
 
int * _confs
 
size_t _confs_no
 
int allDim
 
bool sorted_by_mass
 
bool sorted_by_prob
 
double total_prob
 
size_t current_size
 
double * tmasses
 
double * tprobs
 
int * tconfs
 
int allDimSizeofInt
 

Friends

double AbyssalWassersteinDistanceGrad (FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the)
 

Detailed Description

Definition at line 40 of file fixedEnvelopes.h.

Constructor & Destructor Documentation

◆ FixedEnvelope() [1/4]

ISOSPEC_FORCE_INLINE IsoSpec::FixedEnvelope::FixedEnvelope ( )
inline

Definition at line 57 of file fixedEnvelopes.h.

◆ FixedEnvelope() [2/4]

IsoSpec::FixedEnvelope::FixedEnvelope ( const FixedEnvelope other)

Definition at line 24 of file fixedEnvelopes.cpp.

◆ FixedEnvelope() [3/4]

IsoSpec::FixedEnvelope::FixedEnvelope ( FixedEnvelope &&  other)

Definition at line 35 of file fixedEnvelopes.cpp.

◆ FixedEnvelope() [4/4]

IsoSpec::FixedEnvelope::FixedEnvelope ( double *  masses,
double *  probs,
size_t  confs_no,
bool  masses_sorted = false,
bool  probs_sorted = false,
double  _total_prob = NAN 
)

Definition at line 52 of file fixedEnvelopes.cpp.

◆ ~FixedEnvelope()

virtual IsoSpec::FixedEnvelope::~FixedEnvelope ( )
inlinevirtual

Definition at line 75 of file fixedEnvelopes.h.

Member Function Documentation

◆ AbyssalWassersteinDistance()

double IsoSpec::FixedEnvelope::AbyssalWassersteinDistance ( FixedEnvelope other,
double  abyss_depth,
double  other_scale = 1.0 
)

Definition at line 414 of file fixedEnvelopes.cpp.

◆ addConfILG()

template<bool tgetConfs, typename GenType = IsoLayeredGenerator>
void IsoSpec::FixedEnvelope::addConfILG ( const GenType &  generator)
inline

Definition at line 172 of file fixedEnvelopes.h.

◆ bin()

FixedEnvelope IsoSpec::FixedEnvelope::bin ( double  bin_width = 1.0,
double  middle = 0.0 
)

Definition at line 799 of file fixedEnvelopes.cpp.

◆ Binned() [1/2]

static FixedEnvelope IsoSpec::FixedEnvelope::Binned ( const Iso iso,
double  target_total_prob,
double  bin_width,
double  bin_middle = 0.0 
)
inlinestatic

Definition at line 236 of file fixedEnvelopes.h.

◆ Binned() [2/2]

FixedEnvelope IsoSpec::FixedEnvelope::Binned ( Iso &&  iso,
double  target_total_prob,
double  bin_width,
double  bin_middle = 0.0 
)
static

Definition at line 1088 of file fixedEnvelopes.cpp.

◆ conf()

const int * IsoSpec::FixedEnvelope::conf ( size_t  i) const
inline

Definition at line 100 of file fixedEnvelopes.h.

◆ confs()

const int * IsoSpec::FixedEnvelope::confs ( ) const
inline

Definition at line 90 of file fixedEnvelopes.h.

◆ confs_no()

size_t IsoSpec::FixedEnvelope::confs_no ( ) const
inline

Definition at line 85 of file fixedEnvelopes.h.

◆ empiric_average_mass()

double IsoSpec::FixedEnvelope::empiric_average_mass ( )

Definition at line 1065 of file fixedEnvelopes.cpp.

◆ empiric_stddev()

double IsoSpec::FixedEnvelope::empiric_stddev ( )
inline

Definition at line 113 of file fixedEnvelopes.h.

◆ empiric_variance()

double IsoSpec::FixedEnvelope::empiric_variance ( )

Definition at line 1075 of file fixedEnvelopes.cpp.

◆ FromStochastic() [1/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic ( const Iso iso,
size_t  _no_molecules,
double  _precision = 0.9999,
double  _beta_bias = 5.0,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 230 of file fixedEnvelopes.h.

◆ FromStochastic() [2/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromStochastic ( Iso &&  iso,
size_t  _no_molecules,
double  _precision = 0.9999,
double  _beta_bias = 5.0,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 218 of file fixedEnvelopes.h.

◆ FromThreshold() [1/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold ( const Iso iso,
double  _threshold,
bool  _absolute,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 194 of file fixedEnvelopes.h.

◆ FromThreshold() [2/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromThreshold ( Iso &&  iso,
double  threshold,
bool  absolute,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 183 of file fixedEnvelopes.h.

◆ FromTotalProb() [1/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb ( const Iso iso,
double  _target_total_prob,
bool  _optimize,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 211 of file fixedEnvelopes.h.

◆ FromTotalProb() [2/2]

static FixedEnvelope IsoSpec::FixedEnvelope::FromTotalProb ( Iso &&  iso,
double  target_total_prob,
bool  optimize,
bool  tgetConfs = false 
)
inlinestatic

Definition at line 199 of file fixedEnvelopes.h.

◆ get_total_prob()

double IsoSpec::FixedEnvelope::get_total_prob ( )

Definition at line 192 of file fixedEnvelopes.cpp.

◆ getAllDim()

int IsoSpec::FixedEnvelope::getAllDim ( ) const
inline

Definition at line 86 of file fixedEnvelopes.h.

◆ LinearCombination() [1/2]

FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination ( const FixedEnvelope *const *  spectra,
const double *  intensities,
size_t  size 
)
static

Definition at line 271 of file fixedEnvelopes.cpp.

◆ LinearCombination() [2/2]

FixedEnvelope IsoSpec::FixedEnvelope::LinearCombination ( const std::vector< const FixedEnvelope * > &  spectra,
const std::vector< double > &  intensities 
)
static

Definition at line 266 of file fixedEnvelopes.cpp.

◆ mass()

double IsoSpec::FixedEnvelope::mass ( size_t  i) const
inline

Definition at line 98 of file fixedEnvelopes.h.

◆ masses()

const double * IsoSpec::FixedEnvelope::masses ( ) const
inline

Definition at line 88 of file fixedEnvelopes.h.

◆ normalize()

void IsoSpec::FixedEnvelope::normalize ( )

Definition at line 210 of file fixedEnvelopes.cpp.

◆ operator*()

FixedEnvelope IsoSpec::FixedEnvelope::operator* ( const FixedEnvelope other) const

Definition at line 84 of file fixedEnvelopes.cpp.

◆ operator+()

FixedEnvelope IsoSpec::FixedEnvelope::operator+ ( const FixedEnvelope other) const

Definition at line 63 of file fixedEnvelopes.cpp.

◆ OrientedWassersteinDistance()

double IsoSpec::FixedEnvelope::OrientedWassersteinDistance ( FixedEnvelope other)

Definition at line 358 of file fixedEnvelopes.cpp.

◆ prob()

double IsoSpec::FixedEnvelope::prob ( size_t  i) const
inline

Definition at line 99 of file fixedEnvelopes.h.

◆ probs()

const double * IsoSpec::FixedEnvelope::probs ( ) const
inline

Definition at line 89 of file fixedEnvelopes.h.

◆ reallocate_memory()

template<bool tgetConfs>
void IsoSpec::FixedEnvelope::reallocate_memory ( size_t  new_size)
protected

Definition at line 851 of file fixedEnvelopes.cpp.

◆ release_confs()

int * IsoSpec::FixedEnvelope::release_confs ( )
inline

Definition at line 94 of file fixedEnvelopes.h.

◆ release_everything()

void IsoSpec::FixedEnvelope::release_everything ( )
inline

Definition at line 95 of file fixedEnvelopes.h.

◆ release_masses()

double * IsoSpec::FixedEnvelope::release_masses ( )
inline

Definition at line 92 of file fixedEnvelopes.h.

◆ release_probs()

double * IsoSpec::FixedEnvelope::release_probs ( )
inline

Definition at line 93 of file fixedEnvelopes.h.

◆ resample()

void IsoSpec::FixedEnvelope::resample ( size_t  ionic_current,
double  beta_bias = 1.0 
)

Definition at line 226 of file fixedEnvelopes.cpp.

◆ scale()

void IsoSpec::FixedEnvelope::scale ( double  factor)

Definition at line 203 of file fixedEnvelopes.cpp.

◆ shift_mass()

void IsoSpec::FixedEnvelope::shift_mass ( double  shift)

Definition at line 220 of file fixedEnvelopes.cpp.

◆ slow_reallocate_memory()

void IsoSpec::FixedEnvelope::slow_reallocate_memory ( size_t  new_size)
protected

Definition at line 874 of file fixedEnvelopes.cpp.

◆ sort_by_mass()

void IsoSpec::FixedEnvelope::sort_by_mass ( )

Definition at line 111 of file fixedEnvelopes.cpp.

◆ sort_by_prob()

void IsoSpec::FixedEnvelope::sort_by_prob ( )

Definition at line 123 of file fixedEnvelopes.cpp.

◆ stochastic_init()

template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::stochastic_init< false > ( Iso &&  iso,
size_t  _no_molecules,
double  _precision,
double  _beta_bias 
)

Definition at line 1049 of file fixedEnvelopes.cpp.

◆ store_conf() [1/2]

template<typename T , bool tgetConfs>
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf ( const T &  generator)
inlineprotected

Definition at line 132 of file fixedEnvelopes.h.

◆ store_conf() [2/2]

ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::store_conf ( double  _mass,
double  _prob 
)
inlineprotected

Definition at line 139 of file fixedEnvelopes.h.

◆ swap()

template<bool tgetConfs>
ISOSPEC_FORCE_INLINE void IsoSpec::FixedEnvelope::swap ( size_t  idx1,
size_t  idx2,
ISOSPEC_MAYBE_UNUSED int *  conf_swapspace 
)
inlineprotected

Definition at line 152 of file fixedEnvelopes.h.

◆ threshold_init()

template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::threshold_init< false > ( Iso &&  iso,
double  threshold,
bool  absolute 
)

Definition at line 897 of file fixedEnvelopes.cpp.

◆ total_prob_init()

template<bool tgetConfs>
template void IsoSpec::FixedEnvelope::total_prob_init< false > ( Iso &&  iso,
double  target_prob,
bool  trim 
)

Definition at line 927 of file fixedEnvelopes.cpp.

◆ WassersteinDistance()

double IsoSpec::FixedEnvelope::WassersteinDistance ( FixedEnvelope other)

Definition at line 299 of file fixedEnvelopes.cpp.

◆ WassersteinMatch()

std::tuple< double, double, double > IsoSpec::FixedEnvelope::WassersteinMatch ( FixedEnvelope other,
double  flow_distance,
double  other_scale = 1.0 
)

Definition at line 726 of file fixedEnvelopes.cpp.

Member Data Documentation

◆ _confs

int* IsoSpec::FixedEnvelope::_confs
protected

Definition at line 44 of file fixedEnvelopes.h.

◆ _confs_no

size_t IsoSpec::FixedEnvelope::_confs_no
protected

Definition at line 45 of file fixedEnvelopes.h.

◆ _masses

double* IsoSpec::FixedEnvelope::_masses
protected

Definition at line 42 of file fixedEnvelopes.h.

◆ _probs

double* IsoSpec::FixedEnvelope::_probs
protected

Definition at line 43 of file fixedEnvelopes.h.

◆ allDim

int IsoSpec::FixedEnvelope::allDim
protected

Definition at line 46 of file fixedEnvelopes.h.

◆ allDimSizeofInt

int IsoSpec::FixedEnvelope::allDimSizeofInt
protected

Definition at line 54 of file fixedEnvelopes.h.

◆ current_size

size_t IsoSpec::FixedEnvelope::current_size
protected

Definition at line 50 of file fixedEnvelopes.h.

◆ sorted_by_mass

bool IsoSpec::FixedEnvelope::sorted_by_mass
protected

Definition at line 47 of file fixedEnvelopes.h.

◆ sorted_by_prob

bool IsoSpec::FixedEnvelope::sorted_by_prob
protected

Definition at line 48 of file fixedEnvelopes.h.

◆ tconfs

int* IsoSpec::FixedEnvelope::tconfs
protected

Definition at line 53 of file fixedEnvelopes.h.

◆ tmasses

double* IsoSpec::FixedEnvelope::tmasses
protected

Definition at line 51 of file fixedEnvelopes.h.

◆ total_prob

double IsoSpec::FixedEnvelope::total_prob
protected

Definition at line 49 of file fixedEnvelopes.h.

◆ tprobs

double* IsoSpec::FixedEnvelope::tprobs
protected

Definition at line 52 of file fixedEnvelopes.h.


The documentation for this class was generated from the following files: